tiledb-py v0.31.0

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Name	Upstream Version	Current Version
numpy	2.0.1

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[conda-forge-webservices]

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipe/meta.yaml) and found it was in an excellent condition.

[jdblischak]

Need to do two things:

1. Bump tiledb pin to 2.25
2. Migrate build system to scikit-build-core (see Test scikit-build-core tiledb-py #224)

[dudoslav]

LGTM

[jdblischak]

The current error is:

ERROR: Directory '.' is not installable. Neither 'setup.py' nor 'pyproject.toml' found.

But those files are clearly in the source: https://github.com/TileDB-Inc/TileDB-Py/tree/0.31.0

Maybe they aren't being included in the PyPI source tarball?

[jdblischak]

Maybe they aren't being included in the PyPI source tarball?

No. That's not it.

wget https://pypi.io/packages/source/t/tiledb/tiledb-0.31.0.tar.gz
tar xzf tiledb-0.31.0.tar.gz
## tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.quarantine'
## tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.macl'
## tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.quarantine'
ls tiledb-0.31.0
## CMakeLists.txt   HISTORY.md  PKG-INFO   ci     doc       external  pyproject.toml  tiledb
## CONTRIBUTING.md  LICENSE     README.md  cmake  examples  misc      setup.py

[jdblischak]

Current status:

• linux-*: build immediately fails with ERROR: Directory '.' is not installable. Neither 'setup.py' nor 'pyproject.toml' found.
• osx-64: build passes, tests fail

==================================== ERRORS ====================================
____________ ERROR collecting tiledb/tests/test_pandas_dataframe.py ____________
tiledb/tests/test_pandas_dataframe.py:126: in <module>
    class TestColumnInfo:
tiledb/tests/test_pandas_dataframe.py:148: in TestColumnInfo
    [pd.BooleanDtype()],
E   NameError: name 'pd' is not defined
=========================== short test summary info ============================
ERROR tiledb/tests/test_pandas_dataframe.py - NameError: name 'pd' is not defined
!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!
========================= 1 skipped, 1 error in 2.71s ==========================
WARNING: Tests failed for tiledb-py-0.31.0-py39h83f2935_0.conda - moving package to /Use

• osx-arm64: build passes (tests aren't run when cross-compiling arm64 binaries on an x86 machine)
• win-64: build immediately fails with ERROR: Directory '.' is not installable. Neither 'setup.py' nor 'pyproject.toml' found.

[dudoslav]

This is pretty weird because AFAIK we test if sdists can be installed: https://github.com/TileDB-Inc/TileDB-Py/actions/runs/10099783077

[jdblischak]

This is pretty weird because AFAIK we test if sdists can be installed:

But were any of those tested sdists uploaded to PyPI? AFAICT automatic upload to PyPI was disabled (TileDB-Inc/TileDB-Py#2020), and it wasn't re-enabled prior to tagging 0.31.0

https://github.com/TileDB-Inc/TileDB-Py/blob/0.31.0/.github/workflows/build-wheels.yml#L152

Was the PyPI upload done manually this time? Is that why I am seeing all the tar messages about tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.quarantine'?

[jdblischak]

I think I found the source of the test failure E NameError: name 'pd' is not defined

The code itself was added 2 years ago:

https://github.com/TileDB-Inc/TileDB-Py/blob/0.31.0/tiledb/tests/test_pandas_dataframe.py#L148
TileDB-Inc/TileDB-Py@fd3b808

However, when that code was originally added, pd was defined at the top of the file

https://github.com/TileDB-Inc/TileDB-Py/blob/fd3b80810657225fba41c6fdb3b9a700d52ef1ae/tiledb/tests/test_pandas_dataframe.py#L3

pd = pytest.importorskip("pandas")

But that import was just removed yesterday in TileDB-Inc/TileDB-Py#2016

[jdblischak]

Also, I confirmed that pandas 2.2.2 was installed for the osx-64 builds, which should be compatible with TileDB-Py

[jdblischak]

I was able to build the PyPI source tarball on locally on Ubuntu 22.04:

wget https://pypi.io/packages/source/t/tiledb/tiledb-0.31.0.tar.gz
tar xzf tiledb-0.31.0.tar.gz
python -m venv ./build-pypi
mamba deactivate
source ./build-pypi/bin/activate
cd tiledb-0.31.0/
python -m pip install -v .
## Successfully installed numpy-2.0.1 tiledb-0.31.0

[jdblischak]

Confirmed that the linux-64 and win-64 jobs are failing because extracting the tarball results in a top-level directory (tiledb-0.31.0 and ._tiledb-0.31.0, respectively). Beyond frustrating that this behavior differs across operating systems

[jdblischak]

And I confirmed the previous tarball does the exact same thing on linux:

wget https://pypi.io/packages/source/t/tiledb/tiledb-0.30.0.tar.gz
tar xzf tiledb-0.30.0.tar.gz
ls
## tiledb-0.30.0  tiledb-0.30.0.tar.gz

[jdblischak]

I'm baffled why this is happening. While it is likely due to a difference in the installed tar in the different operating systems, I don't understand why this is happening now.

We could switch from script: to using the individual build.sh and bld.bat, but I don't see how that would make a difference. These just get copied into SRC_DIR and then executed. And from the previous troubleshooting run, SRC_DIR has a top-level directory, so they would just fail. And doing something like cd tiledb-* (but not on macOS since it extracts the tarball fine) would be very hacky.

As a sanity check, I ran grayskull pypi tiledb. It uses the same PyPI URL, and also uses the script field assuming the package has been extracted properly to SRC_DIR.

{% set name = "tiledb" %}
{% set version = "0.31.0" %}

package:
  name: {{ name|lower }}
  version: {{ version }}

source:
  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/tiledb-{{ version }}.tar.gz
  sha256: 4e7fceb44e1e7ade6acfc22bd9085e5c6e2add5891ad268d4246b0265b17b0a1

build:
  skip: true  # [py<38]
  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
  number: 0

[jdblischak]

My only hope is that maybe if the next tarball we upload doesn't produce tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.com.apple.quarantine', then maybe it will extract fine on linux-64 and win-64.

[jdblischak]

tiledb-0.31.0 and ._tiledb-0.31.0, respectively

This was a mistake. I don't know what the purpose of ._tiledb-0.31.0 is on Windows. It is apparently a file. The directory is the same as on linux

 Directory of %SRC_DIR%

07/26/2024  07:13 PM    <DIR>          .
07/26/2024  07:13 PM    <DIR>          ..
07/25/2024  07:40 PM               276 ._tiledb-0.31.0
07/26/2024  07:13 PM               180 bld.bat
07/26/2024  07:13 PM             7,470 build_env_setup.bat
07/26/2024  07:13 PM               311 conda_build.bat
07/26/2024  07:13 PM             2,060 metadata_conda_debug.yaml
07/25/2024  07:40 PM    <DIR>          tiledb-0.31.0

[jdblischak]

These "errors" will go away once they accept the email invitation from GitHub to join this repository

[jdblischak]

It's not pretty, but I did manage to get green CI by:

• Updating all the paths for linux-64 and win-64 to prefix with tiledb-0.31.0
• Applying the fix to the pandas tests from Fix deprecation and test TileDB-Inc/TileDB-Py#2021